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Bruce Eckel's Thinking in Java [mindview.net] is quite handy. You also might appreciate Head First Java [oreilly.com]. (Though the style puts off a lot of people initially, it works really well. I was prepared to hate it.)

I second chromatic's recommendation of Thinking in Java -- it's a little wordy but pretty clear. O'Reilly's Java Cookbook[1] is very good, as is their Java in a Nutshell[2], and Joshua Bloch's Effective Java[3] is a must once you've got some code under your belt. Fowler's Refactoring[4] is also fantastic.

Sun actually has quite a few tutorials on their site [5] that aren't bad.

There are a ton (some say too many) of opensource projects under the Jakarta [6] umbrella. If you're the sort of person who learns by reading other code it's not a bad place to start, particularly some of the simpler projects like commons-lang and commons-collections. You'll wind up getting frustrated because some functionality that takes 10 or 20 lines in Java will in Perl will be one or two.

If you're doing server-side application development I'd recommend spending some time with the Spring framework. [7] It's well-documented, well-designed and strives for simplicity, which is a big difference from many overdesigned Java projects.

Finally, in terms of development environments take a look at IntelliJ IDEA.[8] It's the IDE that got me away from xemacs for Java -- don't think bloated editors like JBuilder, think supersmart and productive. I seriously wish I had this for Perl. Some folks like Eclipse[9] as much as I like IDEA, but IDEA is more polished and straightforward as Eclipse makes you buy into its worldview to get anything done.